Something Dark Over the Sky
by Spinning Furret
Summary: When an experiment goes badly wrong, and a Riolu with the mind of a human lands somewhere in Johto, something is bound to happen. This is the story of what happens.
1. The Psyonograph

**Something Dark Over the Sky**

**Chapter One: The Pysonograph**

**Note: This chapter has been updated to better suit the storyline.**

* * *

One of the people observing the experiment watched as the medic sedated the boy. The first one pointed to the Riolu. "Are you sure a Riolu is the right Pokemon, James?"

James nodded confidently. "Of course, Eric. Out of all Pokemon, Riolu - and their evolution, Lucario - are closest to humans in intelligence and body structure, which is vital for the experiment to succeed.

Eric nodded in agreement. "I would hope that the experiment is successful." The subjects for the experiment - a Riolu and a teen - were inside a special, ultra-secure room. The medic began the process of attaching the necessary to the heads. "We've already gone over budget, and the levels of energy need to make the machine function are astronomical."

"Couldn't Pokemon generate the electricity?" James asked.

Eric shook his head. "The machine has very specific requirements, and Pokemon-generated electricity varies too often in wattage. We're working on a deadline and on thin ice."

"But why couldn't a electric balancer be used? They were made for that very purpose."

"We've spent to much money already and there's nowhere the machine could connect to a balancer. Didn't you read the schematics?" Eric caught himself there. "You don't have the updated schematics yet, do you?"

James shook his head. "Updated schematics?"

Eric chuckled. "The original schematics were incorrect, so as the machine was built they've been updated. Several times now."

There was the sound of a dart hitting a dartboard. James jumped up. The room was dark, and they were tense. Eric chuckled. "That's just the Alakazam. It plays darts."

James composed himself and nodded. "I didn't have much time to read all the papers on the Psyo-transfer Experiment."

Eric shushed him. "Security. The name of the experiment is not to be spoken aloud. Same with the machine."

"Couldn't you use codes?" James said, irritated that nobody had thought to use logic. "Didn't the inventor use his head?"

Eric shook his head. "Codes would make people suspicious. Especially journalists. You know how they love to uncover a story. The official story is that we haven't decided on a name."

"Wouldn't that still make people suspicious?"

"Anybody who comes to close to the lab gets shot. This is a secret even from within." Eric replied coldly. "Stop asking questions."

"What's the Alakazam for?" James pressed.

Eric sighed. "Back-up security procedures. The machine has to store the data of minds, memories, emotions, the entire human and Pokemon intelligence of one member of each species. There wasn't enough memory for any built-in failsafes."

"And I am to assume funding is responsible?"

"My superiors are already unhappy. We've exhausted the last of our funding. Ever since about two months ago, funding has been coming out of the pockets of everyone who's working on this project." Eric explained. "We weren't exactly rich to begin with, and we still have to get food on the table."

James was about to speak again, but Eric didn't give him the chance. "Medic! Ready yet?!"

The medic turned back. "One moment!" He attached the last of the wires. "Ready."

Eric nodded, walking to the control console. He flipped three switches and then pulled the lever, grunting at the strain.

"Vacate the area! Get into the safe room!" Eric shouted. A countdown began, going down from 150. He left and headed towards the safe room.

The safe room was adjunct to the machine room, protected from the machine room in case of a malfunction. To make sure everything could still be seen, there was a large screen of reinforced glass on the walls.

"Eric." James said.

Eric looked at him. "What is it this time?"

"I believe the heating and cooling system is malfunctioning. Haven't you noticed that it's a bit too warm?"

Eric's eyes widened. In the safe room there was an extra control console, as well as the countdown, and a screen that displayed what was happening inside the subject room.

Sure enough, a red light was blinking, indicating that the machine was heating up. Eric sat down at the computer inside the room and began typing, trying to find the source of the error. "I can't fix it." He breathed, sitting back in his chair. "It's a physical malfunction, not one in the programming."

"Calm down." James told him. "The countdown has reached 93."

Eric nodded. He pulled out a portable communicator. "Alakazam, prepare to teleport at my command."

"I'm leaving. I don't want to watch this." The medic said, leaving.

Eric and James stood up and watched through the screen. "We can hope that the heating malfunction doesn't affect the process too badly."

The countdown reached zero, and the transfer began.

Three minutes passed and more lights began blinking. Eric turned to them.

"What's happening?" James asked, noticing the multiple lights blinking.

"Too much heat. And according to these readings, the teen wasn't sedated properly." Eric replied.

"Wasn't sedated properly?" James asked.

The transfer completed a few seconds later. The teen woke up... but he had the mind of a Riolu now, and the feelings, and the memories of a Riolu. It at first seemed calm, but it looked around and saw itself - or rather its body - on the bed next to it, and looking at itself, noticed it was human. The Riolu had been informed of what would happen (so was the teen), of course, to make sure that it didn't panic, but the shock was too much. Panic turned into shock. Eric flipped off the screen. "He's experiencing shock. He won't make it."

"If we had another machine, we could transfer the boy's mind back." Eric added. "Which means we'll have to build one."

"Another machine?"

"This one's broken." Eric said. The lights were off. "The insides got too hot. The wires must've melted." Eric pulled out a communicator. "Teleport." He told the Alakazam.

The Alakazam obeyed, teleporting the Riolu with the mind of teen to Ilex Forest.

"Location?"

_"Ilex Forest in Johto."_ Alakazam told them telepathically before teleporting itself away.

Eric flipped back on the screen. The teen's body lay motionless inside the room, and the Riolu was, of course, not there.

Eric turned a knob on the communicator. "I want the body cryopreserved. And inform the Johto sect that we have a Riolu to find. Its location is Ilex Forest, Johto, though its likely to change. Also inform our Johto sect that the schematics for the Psyonograph will be given to them. Have somebody take the cryopreserved body to Johto. We're going to transfer the mind of the human back to his body. And then we're going to destroy all evidence of this project. Understood?"

* * *

Elsewhere in Ilex Forest, and unconscious Riolu appeared on the ground.


	2. Telepathic Connections

**Something Dark Over the Sky**

**Chapter Two: Telepathic Connections**

**Note: This chapter has been updated to better suit the storyline and personality of the characters.**

* * *

Lock opened his eyes, looking around. _'Where am I?' _He wondered, looking around. It was dark, the trees looked bigger than they should, the grass beneath his feet was damp, and there were many Bug Pokemon going about their business.

It was then that his memory kicked in and he remembered what had happened. He was now a Riolu. Bits and pieces of his memory were missing. He did remember his name: Lock. He remembered his age: 15.

He climbed onto one the trees, looking around. It was rather easy, he thought as he adjusted to his new body. _'But not my new life.'_ He told himself.

He soon got tired, however, and he climbed back down to one of the lower branches and sat down to rest, telling himself not to fall asleep.

...

He woke up several hours later hungry and thirsty. He got down and started to look around for food and water. He sniffed the air, wondering if that would help, and it certainly did. He had forgotten that being in the body of a Riolu gave him all the capabilities of a Riolu.

He followed the scent to a bush of Oran Berries. He picked seven, and headed to the nearby pool of water. Putting the Oran Berries to the side, he knelt down and got some water into his hands and he washed his face.

Lock stared at the water, seeing his reflection for the first time. He cupped some water into his hands and drank. Fresh, and clean water. That meant it likely had some sort of water-cleaning Pokemon in it - his best guess was Gorebyss.

Shaking himself, he picked up the berries and headed back to the tree he'd slept on. He jumped up to one of the lower branches and began to eat while watching what happened near his branch.

A teen with shoulder-length, red hair was making a fire. He wore a sleek midnight blue-purple suit with red lining. Lock continued to eat, wondering if he could get some help from him.

But to do that he'd need to be able to communicate. His mind leaped to telepathy, he thought, enjoying the fifth Oran Berry. And he knew who'd be the guinea pig to see if he could do it. The red-haired teen.

_"Hello? Can you understand me?"_ Lock asked. The teen seemed unaffected. _"It's the Riolu."_ Lock jumped down to the ground. _"Over here, red one."_

The teen turned to him. "Telepathy?"

Lock nodded in confirmation.

"Don't call me red one." He said.

_"Then what is your name?" _Lock asked.

"Silver." He replied.

_"Good to meet you, Silver. I'm Lock."_ Lock walked over and sat down in front of the campfire, across from Silver.

"Pokemon don't name themselves." Silver muttered.

_"I'm not a Pokemon."_ Lock informed him. _"Unbelievable as it may sound. I have a curious mind, and that lead me into a trouble. An assortment of nasty people - the name I can't remember - used a machine to transfer my mind, memory, and emotions to the body of this Riolu. My mind switched with the Riolu's, so did our bodies."_ Lock paused to gather his thoughts.

_"I was unconscious during the entire process. Next thing I know I wake up here. I was told what would happen, probably to make sure I didn't go into shock. They told me more. My Pokemon's memories of their travels with me... wiped. None of them will remember me now. And bits and pieces of my memory is missing." _Lock finished his explanation.

Silver just sat there, processing what Lock had told him. "Why are you telling me?"

_"Because I need help. And because nobody would believe it if you told them."_ Lock told him. _"I am not going to live out my life as a Pokemon."_ He said - well, thought, it is telepathy - with determination.

"And you want me to help you." Silver said. Lock nodded. "Why should I do that?"

Lock's mind went into overdrive trying to create an answer. _"Well, if you were stuck in the body of a Pokemon, you'd want help, wouldn't you?" _Lock was desperate, understandably._  
_

Silver thought for a minute. "Alright. I'll help you get your body back."

Lock let out a breath he didn't know he was holding. _"Thank you very, very much. You have no idea how grateful I am."_

"Under one condition." Silver said. "Stay out of my way. I have things to do in Johto. You stay out of my way. Your problem takes second priority."

Lock nodded. _"Fine by me."_ So long as he got out of the body of a Pokemon and into his own body he could wait.

* * *

Silver stared at Lock. He didn't know why he chose to help him, when he had his own things to do, but it could've been Lock's determination that resonated with his own.

His mind flashbacked to the events of three years ago, when he swore to the man who was - is - his father that he would become a stronger man then him alone.

But to do that he would need Pokemon. He knew Lock wouldn't be willing. He would get himself a Pokemon and become the world's best Pokemon Trainer.

* * *

_"So where are you going?"_ Lock asked, curious. Silver was clearly travelling - it was obvious.

"To get a Pokemon. To become the world's best Pokemon Trainer. To become the strongest, the best. I care little for those who are weak." He spat that last sentence. "Pokemon are power."

Lock shook his head. _"I imagine you wouldn't get along very well with a Magikarp." _Lock chuckled at that. _"Just because one is weak doesn't mean they can't get stronger." _


	3. Pokemon

**Something Dark Over the Sky**

**Chapter Three: Pokemon**

* * *

After Lock had finished telling Silver his tale, and after Silver had agreed to help him get his body back, both of them had settled in to sleep, Lock on his branch and Silver in his sleeping bag.

As Lock rested on his branch, having difficulty getting to sleep, he wondered where in Hoenn he could find the people who did this to him. He sighed, knowing that it would be difficult to get his body back. But he was determined.

* * *

Elsewhere in Johto, on a small rock near the Whirl Islands that was home to the Johto sect of the Organization Shade, the lead scientist studied the schematics for the Pysonograph worriedly. "This is incredible! Absolutely barmy, but incredible!"

"I know." Eric said. "My question is, can you build it?"

"Yes. And I'll certainly do a lot better than you Hoenn sects." The lead scientist muttered. "Now scram already, I've got people to talk to if you want this built."

Eric's eye twitched and he turned around, walking out of the room.

"Just a moment." The lead scientist said as Eric reached the door's threshold. "Why do you need another one of these after the last one failed so badly?"

"This project is being abandoned. All evidence of it destroyed. Before we do that, however, we have to right our wrongs." Eric said.

* * *

"Wake up." Lock heard, opening his eyes blearily. _"It's too early..." _"I said wake up!" Silver repeated and Lock opened his eyes, stretching. "Finally awake, are you? Get up. We're leaving."

_"Where to?"_ Lock asked.

"Goldenrod City. It has a high-speed Magnet Train. That's how I get to Cherrygrove City, from there, New Bark Town. That's where I get a Pokemon." Silver gave a small smile at the thought.

_"How do you intend to get it?"_

"I take the Pokemon and it's mine." Silver replied.

_"Petty theft, basically."_ Lock deadpanned.

The remainder of the journey to Goldenrod, and then Cherrygrove was silent.

* * *

From Cherrygrove City it was short walk to New Bark Town. Silver observed the lab through a side window, scheming on how to steal a Pokemon. Lock sat on a nearby tree branch, watching the goings-on.

At one point, a new Trainer came investigating. "Oi, you. Why are you hanging around here like that? Are you looking to steal one of the Pokemon?"

"Mind your own business." Silver told him rudely. "Shoo." He gestured to the trainer to leave.

After that trainer left New Bark Town, Silver sneaked in and took a Pokemon, choosing a Totodile. "What are you doing with that?" Professor Elm noticed.

Silver smirked and ran. Lock followed, jumping across trees. _"If you'd just asked, you probably would've gotten a Pokemon." _Lock sighed.

Silver ignored him. They soon reached the entrance to Cherrygrove City, Silver collided with the trainer who'd gotten a Pokemon at the Lab.

"You're that guy that was hanging around the Lab!" The trainer said, immediately recognizing Silver. "You stole one of the Pokemon, didn't you? Professor Elm might want it back."

"Yes, I did get a Pokemon. The Pokemon you got is too good for someone like you." Silver said.

"Gold." The trainer said. "My name is Gold. And I'll be taking the Pokemon back to Professor Elm." Inspiration struck him. "How about a Pokemon battle first?"

"Get out of my way." Silver said, but Gold stood in front of him. "A Pokemon battle." Gold said again.

"Fine." Silver muttered, letting out his Totodile.

"Let's go, Cynder!" Gold said, letting out his Cyndaquil to battle. "Tackle!"

"Dodge it and use Scratch!" Silver ordered. Totodile leaped out of the way as Cynder skidded to a halt, before leaping back into the fray and scratching the Pokemon.

"Tackle!" Gold ordered just after Totodile finished. Cynder got the advantage of surprise, throwing itself into the Pokemon, before standing up looking very pleased as Totodile was knocked back.

"Scratch again!" Silver called. "Dodge it and Tackle!" Gold said. Totodile ran to Cynder to attack, but just then Cynder jumped out of the way before tackling it again. "Scratch!" Totodile shook itself and jumped to Cynder, scratching it again.

Both of the Pokemon showed signs of fatigue, but Totodile looked to be in better condition. "Again!" Silver called. Totodile dashed towards Cynder, scratching yet again.

_"And the finishing blow..." _Lock grinned as Totodile gave one last scratch. Cynder fell forward, unconscious.

"Return, Cynder." Gold sighed. "You did well." He put the PokeBall away. "Not bad."

Silver returned Totodile to its PokeBall. "Excellent. A strong one for sure." He told himself. "Listen to me. Stay out of my way, Gold, if you know what's good for you."

"Who are you, anyway?"

"My name is Silver. I am going to be the world's strongest Pokemon trainer. Stay out of my way." Silver said, leaving.

_"Ah, a Totodile. My congratulations. I myself got a Treecko when I started out. Something of a loner, it must be said, but fast, strong, and effective. One of my best friends - we knew each other very well, so well we didn't need words to communicate. Professor Birch called it an unbreakable bond, Trainer and Pokemon. Those were the days..."_ Lock reminisced. _"You ought to get Totodile healed at a Pokemon Center. I don't think any of us would say no to food,_ _either." _

Silver nodded in agreement. "We're going to a Pokemon Center. From there, Violet City."

_"What will you do there?"_ Lock asked.

"Challenge the Gym Leader and take the Sprout Tower Trial." Silver responded.

_"Sprout Tower Trial?" _

"A challenge for Trainers to beat before they face the Gym Leader. Supposedly the Tower was made out of a 100-foot tall Bellsprout." Silver sneered at that. "Myth and legend, of course."

_"Myth and legend always have a foundation in truth somewhere along the line."_ Lock advised. _"It could have easily been a 100-foot tall tree. They do exist."__  
_

Silver ignored him.

* * *

**Author's Note: **I seem to have adopted the policy of taking previous chapters and refining them. I hope this doesn't cause too much inconvenience.


	4. Sprout Tower

**Something Dark Over the Sky**

**Chapter Four: Sprout Tower**

* * *

Silver walked in to the first floor and headed for the stairs. One of the Sages stood in front of it. "Welcome. Do you wish to take the Sprout Tower Challenge? Once you enter you may not leave until you win or until you lose."

"Yes." Silver replied. Lock looked around, walking around.

"Then enter to the second floor and defeat every Sage there to prove your trust in your Pokemon." The Sage bowed again, stepping aside.

Silver ignored him and ascended. Another Sage stood at the stairs. "I, Sage Nico, will be your first opponent." The Sage bowed. "Bellsprout, you're up!"

"Totodile! Defeat him!" Silver said, throwing the PokeBall and letting out his Pokemon. "Use Bite!" Totodile bit the Pokemon.

"My young friend, you are at a disadvantage. I wonder if you can still emerge the victor." Nico chuckled. Lock laughed at that. "Bellsprout, use Vine Whip." Nico commanded.

"Dodge it and use Scratch!" Silver ordered. Totodile dashed towards the Bellsprout and scratched furiously. "Vine Whip!"

The long, thin vine lashed out to Totodile sharply, knocking the Pokemon back. Totodile growled. "Tackle!" Silver called. Totodile nodded curtly to him before jumping into the Bellsprout.

"Vine Whip!" Sage Nico commanded. "Dodge it!" Totodile barely managed to avoid it. "Again!" Nico called. "Dodge it and use Bite!" Silver returned. Totodile again just barely jumped out of the the way before dashing to it and biting. The Bellsprout fell unconscious. "As you can see, I am victorious." Silver smirked.

"Return, Bellsprout." Nico said. "You have done well. Now return to the first floor and face your next opponent." Nico bowed to him, directing him to the right.

Lock threw an Oran Berry to Totodile, who greedily and eagerly ate it as Silver returned him to his PokeBall.

And so they descended to the first floor. "I, Sage Chow shall be your next opponent. In this Tower we honor the tradition of befriending Pokemon to express our gratitude for what they do for us. Do you understand what I mean?" Sgae Chow asked. "No matter. Bellsprout, come out and fight!" Chow let out his Bellsprout.

"Totodile, take him out!" Silver called, letting out his Pokemon. "Use Bite!"

"Dodge and use Vine Whip!" Chow countered as Totodile leaped forward to bite Bellsprout. Bellsprout got out of Totodile's way as fast as it could using its spindly little legs, and then lashed a vine out to Totodile.

"Again!" Silver called out. "Vine Whip!" Chow returned. "Dodge it!" Silver responded. Totodile grinned and leaped out of the way of the vine before dashing back in to the fray to bite Bellsprout on the leg.

The Grass-type flinched at the attack. "Use Ingrain!" Chow commanded. Bellsprout released several roots out of its arms and into the floor of the Tower, rendering itself incapable of motion.

"Scratch!" Silver ordered. Totodile dashed forward and scratched the Bellsprout right on its bell-like head. "Vine Whip!" Chow called. "Dodge it and Bite!" Silver countered. The vine shot out and Totodile jumped out of the way before running at Bellsprout, ready to bite it. "Again!" Chow said, and this time the vine hit its target.

Both showed signs of fatigue, but Totodile looked more tired. "Shake it off and attack!" Silver said, uncaring about Totodile's plight. Totodile nodded with a grim determination and tackled Bellsprout, breaking the roots. The Bellsprout, unable to heal itself and hit with a head-on attack, fainted.

"Return, Bellsprout." Chow said. "You did excellently." He said, looking at the PokeBall. He put the PokeBall away and looked at Silver. "You do not appreciate your Pokemon as you should, nor do you feel any emotion. Pokemon are to be befriended to bring out their inner strength."

Silver looked coldly at Chow. "The fact remains that I still defeated you despite your claims."

Chow nodded. "Yes. Regardless of my own misgivings, you have came out the victor. Ascend again to the second floor to face your next opponent."

Silver walked up the stairs to the second floor.

"I, Sage Edmund, will be your opponent. They say eyes are windows into the soul. For Pokemon, eyes are doorways into the soul. Let's go, Gastly!" Edmond said, letting out Gastly, who hissed at Silver and then disappeared.

"Totodile, defeat him!" Silver called, letting out the Totodile. Lock threw an Oran Berry to the Pokemon again. Sage Edmond smiled at the Riolu. "Use Lick!" Edmond commanded.

The Gastly reappeared in front of Totodile, tongue out and ready to lick.

"Dodge it and use Bite!" Silver called, not a moment too soon. Totodile jumped out of the way and then proceeded to take the gaseous Pokemon by surprise, biting it harshly. It was very effective.

"You know your type match-ups well." Edmond remarked. "Hypnosis!" Gastly disappeared and reappeared in front of Totodile. Its eyes were now pulsing yellow and red and slowly swirling. Totodile stared at it, enthralled.

"Snap out of it and Bite!" Silver shouted out. Totodile shook its head and bit the Gastly right then and there. The Pokemon fell to the ground, unable to battle any longer. "Return, Gastly." Edmond sighed. "Well done, my friend." He put the PokeBall away. "You are uncaring to the plight of your Pokemon when they fight. Your methods of training are clearly unworthy. You must befriend your Pokemon, it is not a slave. Regardless, you may go on to the third floor, where your last opponents wait."

Silver walked up the stairs without a word.

A rather severe-looking Sage looked at Silver. "I, Sage Lucien, shall be your opponent." Lucien had two PokeBalls in his hand. "Prepare yourself. I am not as easily defeated as my colleagues on the lower floors. Go, Hoothoot!"

"Totodile, defeat him!" Silver again sent out his only Pokemon to fight. "Use Bite!"

"Hoothoot, ascend!" Lucien called, and Hoothoot flew up into the air. "Now use Peck!" Hoothoot shot downwards, beak pointed straight at Totodile.

"Dodge it and Bite!" Silver ordered. Hoothoot's attacked missed as Totodile jumped to the side before jumping closer to Hoothoot and biting the Flying-type before it could get back to the sky. Hoothoot flew back upwards. "Water Gun!" Silver ordered, wondering if Totodile knew this attack yet.

Totodile seemed to smirk as he shot a jet of water towards the airborne Pokemon, knocking it to the ground. "Now use Bite!" Totodile responded with a nod of affirmation, running to Hoothoot and biting it.

The Hoothoot fell unconscious. "Return, Hoothoot." Lucien said.

"What was that about difficulty you were saying?" Silver said, smirking.

Lucien glared. "You have dispatched with my first Pokemon easily. The second will not be so easy. Bellsprout, come on out!" Lucien let out a Bellsprout to fight. "Vine Whip!"

A vine lashed out and hit Totodile seconds later. This Bellsprout was much stronger than the ones on the lower floors. "Use Bite!" Silver ordered.

"Vine Whip!" Lucien called out. Bellsprout didn't allow Totodile to get close enough to attack.

"Water Gun!" Silver called, switching to a different tactic. "Aim for the eyes!" Totodile shot a jet of water straight at the eyes. Bellsprout cried out in pain, immediately closing them, rendering the Pokemon blind. "Use Wrap!" Lucien called. Bellsprout sent vines towards Totodile - still in front of it - wrapping it in vines.

"Get out of there!" Silver called, Totodile struggling to get out of the vines.

"Vine Whip!" Lucien called out, taking advantage of Totodile's immobility. "Again!" Two vines lashed out on Totodile.

"Scratch your way out if you must!" Silver ordered, somewhat annoyed. Totodile obeyed and soon got out. "Bite! Stay out of the line of fire!" Silver called. Totodile jumped to the side and then dashed towards Bellsprout, biting it harshly. "Vine Whip!" Lucien ordered. Bellsprout turned to where Totodile had came from shot out a vine. It hit Totodile easily.

"Let's finish this! Vine Whip once more!" Lucien said. "Dodge it and use Scratch!" Bellsprout shot out another vine. Totodile jumped out of the way and charged towards Bellsprout, scratching it angrily.

Bellsprout fell unconscious. "Return, Bellsprout." Lucien stared at the PokeBall for a moment before putting it away. "How harsh and unhelpful you are to your Pokemon. Nevertheless, I step aside and allow you to face your next foe." Lucien told him.

Silver first used a Potion on Totodile, healing it. Totodile grinned at Silver, seeming to thank him. Silver ignored it.

Sage Lucien stepped aside and a different Sage walked in, ready to battle. "I, Sage Troy, will be your penultimate opponent. In this Tower we strive to befriend the Pokemon that live here and the Pokemon we train. We do so as an expression of our gratitude to respect them for everything they do for us. Without the friendship and alliance Pokemon have with us, the human species would have never survived to present day. It is for that reason that this Tower exists. You will face me now. Bellsprout, let's fight!"

"Totodile, use Bite!"

"Vine Whip!" Before Totodile could even attack a vine lashed out, striking the Pokemon.

"Water Gun!" Silver called. Totodile shot out a jet stream of water which hit the Bellsprout, knocking it down. "Bite!" Totodile ran to Bellsprout while it was still down and proceeded to bite it rather nastily.

Troy smiled. "It won't be that easy to defeat my Pokemon. Vine Whip!" He called. Bellsprout again lashed out with another vine. "Dodge it!" Totodile jumped out of the way.

"Again!" Troy ordered. Bellsprout lashed another vine out, striking Totodile again.

"Water Gun and then Bite!" Silver called out. Totodile shot a jet of water towards the Bellsprout and then ran forward and bit it, similar to how it did earlier.

"Vine Whip!" Troy commanded. Bellsprout responded with a particularly fast vine that lashed Totodile. "Again!" Troy called. "Don't let up!" Bellsprout lashed again and again, battering Totodile.

"Hang in there! Dodge and use Bite!" Silver ordered. Totodile leaped out of the way of one of the vines, running to Bellsprout and chomping it. "Scratch!" Silver ordered. Totodile nodded and obeyed. "Again!" Totodile repeated the motions.

Finally, Bellsprout succumbed. "Return, Bellsprout." Sage Troy said. "You have done well to get this far. Your final opponent will be the Elder himself. Your Pokemon will be healed."

Silver returned Totodile to its PokeBall and handed it to Sage Troy, who applied a Potion, healing all of Totodile's wounds.

Sage Troy stepped aside. An older man, with very hairy eyebrows and mustache, and a sharp gaze about him walked forward slowly. "So good of you to come here. Sprout Tower is a place of Training. People and Pokemon test their bonds to see if they can build a bright future together. I am the final test." The Elder pulled out three PokeBalls. "I have seen your battling and I must say I am disappointed that someone so young could be so harsh and unnecessarily unkind. Despite that, you have prevailed against each and every test put before you. I, Elder Li, shall be your final opponent. But this will not be the type of battle you are used to. Instead, a series of trials." A Bellsprout came out of the PokeBall.

"This will be your first one. The Trial of Trust. The Bellsprout will Ingrain itself into the floor. You must defeat it."

"That sounds easy." Silver smirked.

"Not so." Elder Li said. "Your Pokemon won't be able to get close. There will be vines waiting for it, lashing out. You must figure out how to defeat it."

"Show him what we've got, Totodile!" Silver let out his Pokemon.

"Use Ingrain! And if that Totodile comes close use Vine Whip!" Elder Li ordered.

Bellsprout released a series of roots and vines into the ground, its own legs becoming roots into the floor.

"Use Bite!" Totodile nodded and ran forward. Bellsprout immediately unleashed a vine. "Dodge it!" Silver ordered. Totodile leaped out of the way, but once the first vine retracted another one came for Totodile, hitting it.

The vines were very fast. "Get out of the way!" Silver ordered. He wouldn't have his Pokemon defeated after he'd come this far. Totodile leaped out of the way, watching the rather smug Bellsprout with a weary eye.

_"Don't tell me you can't figure even this out..."_ Lock telepathically muttered, having already solved it. Silver ignored him, mind working overtime. It seemed that he'd found an answer when he smirked. "The vine's on a one-path trajectory... and only one vine at a time... well, I guess that means...

"Totodile, bite one of the vines! And when you get in close, attack!" Silver ordered.

Totodile looked at Silver as though he was insane.

_"Now we've got it... the question is, will Totodile obey?"_ Lock asked, more to himself than anything.

"Just do it!" Silver said.

Elder Li smiled darkly. "And that's the trial! Does your Pokemon trust you enough to obey... more importantly, do you trust Totodile enough to pull it off?" Elder Li chuckled.

"Do it now!" Silver ordered. "Bite the vine, and then when you get in close, Bite the Bellsprout!"

_"Bite the Bellsprout... catchy."_ Lock laughed.

Totodile nodded, trusting Silver. The Pokemon got in close, stepped to the side so the vine didn't hit him, bit the vine, and now that he had reached the Bellsprout, began to Bite and Scratch furiously.

"Vine Whip!" Elder Li ordered. Bellsprout lashed, knocking Totodile far away. It was a stronger Bellsprout than what they'd faced before.

"Again!" Silver ordered. Totodile leaped forward, and bit the vine. "Vine Whip!" Li ordered. Another vine shot out, ruining their plan.

But Silver, it seemed had already figured it out. "Again!" He ordered. Totodile bit the vine again. Another vine shot out. "Bite that one!" Silver ordered. Totodile bit the second vine and again got in close to the Bellsprout, furiously attacking.

Bellsprout fainted. "Return, Bellsprout." Li put the PokeBall away. "Well done, boy. Perhaps there is hope for you yet. Your trust in your Pokemon - and the Pokemon's trust in you - has proven one of ties you and your Pokemon share. Your next test will be the Trial of Ingenuity. This tests your intelligence as a Trainer to adapt to new situations and think on the spot, in the heat of battle." Elder Li let out a Hoothoot. "Hoothoot, ascend!"

Hoothoot flew up into the air. "Use Aerial Ace!" Li ordered.

Hoothoot flew down and a fast speed towards Totodile, knocking it to the ground. "Totodile, use Water Gun!" Silver ordered as Hoothoot ascended again. "Gun it out of the sky!"

Totodile nodded and shot a jet of water at the Flying-type. Hoothoot remained in the air. Silver frowned, thinking. "Use it three times! Three jets, short but deadly!" Totodile obeyed and it knocked the Hoothoot out of the sky.

"Now attack! Scratch it and Bite it!" Silver commanded. Totodile dashed to the Pokemon and did indeed attack it.

"Back into the air!" Elder Li called, and Hoothoot once again became airborne. "Aerial Ace!"

"Bite it as it comes down!" Silver countered. Hoothoot came down quickly. Totodile got out of the way, biting its leg as it became airborne. Hoothoot hovered in the sky, Totodile stubbornly attached to its leg through sheer force of muscle, Hoothoot shaking its leg to try and get it off. Totodile finally let go as Hoothoot brought out its other foot to push it down.

"Use Hypnosis!" Elder Li said. Hoothoot came down slowly, its eyes pulsing red and yellow and ever so slowly swirling. Totodile stared into its eyes, becoming sleepier.

"Bite it!" Silver called. Totodile continued to stare, enthralled. "Bite it now!" Totodile was caught in the alluring, pulsing colors of it.

"I said Bite it! You obey me!" Silver said. Totodile snapped out of it and bit Hoothoot right then and there. Hoothoot fell, unconscious.

"Return, Hoothoot." Elder Li said. "Excellent. You may do well as a Trainer - your ingenuity and intelligence proven, and the trust you both have in each other reinforced in it. The final trial - having proven trust and intelligence - will be of strength. The Trial of Strength. Let's go Gastly!"

Gastly appeared, hissing and moaning and groaning and generally being very annoying, before disappearing. "Use Toxic!" Elder Li ordered. Gastly appeared, and some of the gas around it detached from Gastly and entered Totodile. "You have a limited time to defeat Gastly. Toxic poisons badly."

And it looked that way too. Totodile looked worse than before, and it had already suffered damage of previous battles.

"We need to end this quickly." Silver muttered.

"Use Lick!" Li ordered. Gastly appeared in front of Totodile. "Bite it now!" Silver ordered before Gastly could attack. Totodile bit and it bit hard. Gastly gave an unearthly scream and disappeared. "Use Smog!" Li called.

Gastly reappeared and gave an alien laugh before its gas began to seperate and become a black smog, with its own gas replenishing itself. Gastly disappeared. The smog dealt damage, and Totodile was panting. "Lick!"

"Bite it!" Silver said, and again Totodile attacked before Gastly could. Gastly fainted. "Return, Gastly. You have completed the trials. Allow me to heal your Pokemon." Silver returned Totodile to its PokeBall and handed it to the Elder. The Elder applied a Super Potion to it. The PokeBall absorbed the medicine and healed Totodile.

The Elder sighed. "You've shown us what you've got, and it is indeed exceptional... You may have the TM Flash. You need to care for your Pokemon more. The bond between Pokemon and Trainer is what truly brings out its inner strength. The way you treat your Pokemon is too harsh. Pokemon are not tools of war. You may not be listening now, but you will one day face an opponent so powerful that you will have to put some thought into how you treat your Pokemon." Elder Li lifted a gnarled finger and pointed at Silver. "Mark my words, boy, the future holds only loss for you unless you learn to befriend your Pokemon. You may take that staircase over there to leave." He pointed at a staircase to the left.

The Elder left to a machine behind him, presumably to heal his Pokemon. It was the same machine Pokemon Centers used. "Excellent battling, I must say."

Silver turned around to see Gold. "Excellent battling indeed, but the Elder has a point."

"He calls himself the Elder. But he was no match for me. Sure enough, those who say one should be nice to Pokemon lose to me." Silver smirked. "All I care for is strong Pokemon. The rest are meaningless."

Gold just shook his head.

* * *

_"I've remembered the name of the people who did this to me." _Lock informed Silver as he walked down the staircase to the first floor.

"Who?" Silver asked, genuinely curious.

Lock looked unusually grim. _"The Organization Shade."_

"The Organization Shade?"

_"I don't know much, but I intend to research at the Pokemon Center using the computer."_ Lock told him.

Silver nodded.

* * *

_"The Organization Shade, from what I can gather, is a mysterious group of people that has been conduction illegal experiments on Pokemon for years. The International Police hasn't gotten involved because the Organization stays low-profile. It's got some powerful backers, including former members of Team Rocket, Magma, Aqua, and even some defects from Team Galactic and Team Plasma. Now, mind you, most of the time these great big evil teams are foiled by some new Trainer with an unbreakable bond with his Pokemon, but those are high-profile teams._

_"Organization Shade takes a different route. It stays low and doesn't make too much of a fuss in the media. So nobody's come knocking their door to single-handedly disband them. I found them - a chance encounter with them taking a Pokemon. My curiosity lead me to their base. And the result... well, you're looking at it now." _Lock explained. _"Their Johto sector is located around the Whirl Islands. Since you'll be going their anyway, I see it as a very good opportunity to see if I can get my body back."_

Silver nodded. "Yes, we'll do that. Then I won't have your problem on my shoulders."

_"Exactly."_ Lock muttered, voice dripping with sarcasm.

* * *

**Author's Note: **Well, that's that for the longest chapter I've ever written. Hope you enjoyed. Next chapter: Silver battles Falkner, Lock complains about the PokeGear, and somebody's looking for a missing Riolu.


	5. Notation from the Author

**Notation From the Author:**

* * *

I'm afraid that for the remainder of January and possibly February chapters will arrive rather slower than they have. This is because of my main job in the outside world, as Editor-in-Chief of a new video gaming magazine called Up-Down-Left-Right, you can find it at Facebook.

Regardless, I make it clear this story is not abandoned - merely chapters will have longer stretches of time between delivery. You are thanked for your cooperation and understanding in this manner.

-Generic Fanfi-  
-Spinning Furret


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